M Scott Shell

Summary

Affiliation: University of California
Country: USA

Publications

  1. doi request reprint Systematic coarse-graining of potential energy landscapes and dynamics in liquids
    M Scott Shell
    Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106 5080, USA
    J Chem Phys 137:084503. 2012
  2. pmc A test on peptide stability of AMBER force fields with implicit solvation
    M Scott Shell
    Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106 5080, USA
    J Phys Chem B 112:6878-86. 2008
  3. doi request reprint The relative entropy is fundamental to multiscale and inverse thermodynamic problems
    M Scott Shell
    Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
    J Chem Phys 129:144108. 2008
  4. pmc Blind test of physics-based prediction of protein structures
    M Scott Shell
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA
    Biophys J 96:917-24. 2009
  5. pmc The protein folding problem
    Ken A Dill
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
    Annu Rev Biophys 37:289-316. 2008
  6. doi request reprint A new multiscale algorithm and its application to coarse-grained peptide models for self-assembly
    Scott P Carmichael
    Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
    J Phys Chem B 116:8383-93. 2012
  7. pmc Smoothing protein energy landscapes by integrating folding models with structure prediction
    Ari Pritchard-Bell
    Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
    Biophys J 101:2251-9. 2011
  8. doi request reprint Can peptide folding simulations provide predictive information for aggregation propensity?
    Edmund I Lin
    Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106 5080, USA
    J Phys Chem B 114:11899-908. 2010
  9. pmc The search for the hydrophobic force law
    Malte U Hammer
    Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
    Faraday Discuss 146:299-308; discussion 367-93, 395-401. 2010
  10. doi request reprint Molecular insights into diphenylalanine nanotube assembly: all-atom simulations of oligomerization
    Joohyun Jeon
    Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106 5080, USA
    J Phys Chem B 117:3935-43. 2013

Collaborators

Detail Information

Publications14

  1. doi request reprint Systematic coarse-graining of potential energy landscapes and dynamics in liquids
    M Scott Shell
    Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106 5080, USA
    J Chem Phys 137:084503. 2012
    ....
  2. pmc A test on peptide stability of AMBER force fields with implicit solvation
    M Scott Shell
    Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106 5080, USA
    J Phys Chem B 112:6878-86. 2008
    ..Overall, this work indicates that some of these all-atom physics-based force fields may be good starting points for protein folding and protein structure prediction...
  3. doi request reprint The relative entropy is fundamental to multiscale and inverse thermodynamic problems
    M Scott Shell
    Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
    J Chem Phys 129:144108. 2008
    ....
  4. pmc Blind test of physics-based prediction of protein structures
    M Scott Shell
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA
    Biophys J 96:917-24. 2009
    ..This approach may also be useful for predicting physical protein folding routes, non-native conformations, and other physical properties from amino acid sequences...
  5. pmc The protein folding problem
    Ken A Dill
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
    Annu Rev Biophys 37:289-316. 2008
    ....
  6. doi request reprint A new multiscale algorithm and its application to coarse-grained peptide models for self-assembly
    Scott P Carmichael
    Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
    J Phys Chem B 116:8383-93. 2012
    ..In particular, we present results for a polyalanine case study, with attention to both individual peptide folding and large-scale fibril assembly...
  7. pmc Smoothing protein energy landscapes by integrating folding models with structure prediction
    Ari Pritchard-Bell
    Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
    Biophys J 101:2251-9. 2011
    ..Conversely, detailed predictions of structures and the relative entropy approach enable one to extract coarse topographic features of protein landscapes that may enhance the development and application of simpler folding models...
  8. doi request reprint Can peptide folding simulations provide predictive information for aggregation propensity?
    Edmund I Lin
    Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106 5080, USA
    J Phys Chem B 114:11899-908. 2010
    ..Importantly, these models quantify the importance of different molecular properties in aggregation driving forces; notably, they suggest that hydrophobic interactions play a dominant role...
  9. pmc The search for the hydrophobic force law
    Malte U Hammer
    Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
    Faraday Discuss 146:299-308; discussion 367-93, 395-401. 2010
    ..Such a model may be useful for theoretical studies of the HI over the broad range of scales observed in SFA experiments...
  10. doi request reprint Molecular insights into diphenylalanine nanotube assembly: all-atom simulations of oligomerization
    Joohyun Jeon
    Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106 5080, USA
    J Phys Chem B 117:3935-43. 2013
    ....
  11. pmc Charge effects on the fibril-forming peptide KTVIIE: a two-dimensional replica exchange simulation study
    Joohyun Jeon
    Department of Chemical Engineering, University of California, Santa Barbara, California, USA
    Biophys J 102:1952-60. 2012
    ..Our results suggest that sequence changes can have significant effects on self-assembly through not only direct peptide-peptide interactions but conformational entropies and degeneracies as well...
  12. ncbi request reprint Coarse-graining errors and numerical optimization using a relative entropy framework
    Aviel Chaimovich
    Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106 5080, USA
    J Chem Phys 134:094112. 2011
    ..Finally, we demonstrate the application of these theoretical considerations and algorithms to a simple, instructive system and characterize convergence and errors within the relative entropy framework...
  13. doi request reprint Two-dimensional replica exchange approach for peptide-peptide interactions
    Jason Gee
    Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106 5080, USA
    J Chem Phys 134:064112. 2011
    ..The results for these systems are compared to those from conventional REMD simulations, and demonstrate good convergence properties, low statistical errors, and, for the leucine zippers, an ability to sample near-native structures...
  14. ncbi request reprint Computational characterization of the sequence landscape in simple protein alphabets
    M Scott Shell
    Department of Chemical Engineering, Princeton University, Princeton, NJ 08544, USA
    Proteins 62:232-43. 2006
    ..Our calculations suggest that model-specific features can have a profound effect on protein design algorithms, and our methods offer a number of ways by which sequence landscapes can be quantified...